What's wrong with the flag to anyone? I'm a progressive atheist, and I don't have any problem with it. I've never heard of anyone with a problem with it. All nations have a flag. The other 3 examples you cited were about respecting everyone's right to worship as they please, which is spelled out explicitly in the Constitution of the United States. There's nothing in the constitution about flags. If we slapped a big "In god we trust" on it, then we'd have a problem.
Prayer in school, Christmas, and the money line are all violations of the founding documents of this country. The flag is not. Atheist progressive don't hate you or your way of life, at least not true atheist progressives. We're not here just to piss in your Cheerios. In fact it's our Cheerios that have received the most urination in the last 50 years by having god forced on us. It's the opposite of freedom to have religion forced on someone.
That's not to say that someone might decide for themselves not to salute the flag, or feel the need to respect it. On it's face though, the flag is not offensive in any way that I can think of.
I don't understand why it's become such a culture war to say "Happy Holidays" instead of "Merry Christmas". HH simply means your extending your best wishes to all cultures that call themselves American, whereas MC excludes about 30% of the population. I've no beef with Christmas. I celebrate it as a national holiday. Santa Claus isn't a religious figure, and nativity scenes that people put up in their yards are their personal choice. I don't begrude them their religious beliefs in the slightest.